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    219 results match your criteria Bioinformatics and Biology Insights [Journal]

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    Finding the Sources of Missing Heritability within Rare Variants Through Simulation.
    Bioinform Biol Insights 2017 4;11:1177932217735096. Epub 2017 Oct 4.
    BDX Research & Consulting LLC, Fairfax, VA, USA.
    Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. Read More

    A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines.
    Bioinform Biol Insights 2017 27;11:1177932217733422. Epub 2017 Sep 27.
    Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.
    The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. Read More

    Bioinformatics Study of m.9053G>A Mutation at the ATP6 Gene in Relation to Type 2 Diabetes Mellitus and Cataract Diseases.
    Bioinform Biol Insights 2017 12;11:1177932217728515. Epub 2017 Sep 12.
    Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia.
    The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the ATP6 gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Read More

    Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.
    Bioinform Biol Insights 2017 13;11:1177932217720405. Epub 2017 Jul 13.
    Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
    The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (RkNN) search. Read More

    CellTrans: An R Package to Quantify Stochastic Cell State Transitions.
    Bioinform Biol Insights 2017 16;11:1177932217712241. Epub 2017 Jun 16.
    Fakultät Informatik/Mathematik, Hochschule für Technik und Wirtschaft Dresden, Dresden, Germany.
    Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. Read More

    A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major.
    Bioinform Biol Insights 2017 12;11:1177932217712471. Epub 2017 Jun 12.
    Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.
    We present an approach for detecting enzymes that are specific of Leishmania major compared with Homo sapiens and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for L major compared with H sapiens, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of L major and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with H sapiens. Read More

    Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows.
    Bioinform Biol Insights 2017 28;11:1177932217704667. Epub 2017 Apr 28.
    Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
    In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Read More

    In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.
    Bioinform Biol Insights 2017 18;11:1177932217702388. Epub 2017 Apr 18.
    Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.
    Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. Read More

    An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of Cymbopogon winterianus.
    Bioinform Biol Insights 2017 30;11:1177932217701735. Epub 2017 Mar 30.
    Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India.
    Citronella (Cymbopogon winterianus) is one of the richest sources of high-value isoprenoid aromatic compounds used as flavour, fragrance, and therapeutic elements. These isoprenoid compounds are synthesized by 2 independent pathways: mevalonate pathway and 2-C-methyl-d-erythritol-4-phosphate pathway. Evidence suggests that 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-controlling enzyme for the synthesis of variety of isoprenoids. Read More

    PISMA: A Visual Representation of Motif Distribution in DNA Sequences.
    Bioinform Biol Insights 2017 30;11:1177932217700907. Epub 2017 Mar 30.
    Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City, México.
    Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. Read More

    Plasma MicroRNA Levels Following Resection of Metastatic Melanoma.
    Bioinform Biol Insights 2017 23;11:1177932217694837. Epub 2017 Feb 23.
    Department of Surgery, The Ohio State University, Columbus, OH, USA.
    Melanoma remains the leading cause of skin cancer-related deaths. Surgical resection and adjuvant therapies can result in disease-free intervals for stage III and stage IV disease; however, recurrence is common. Understanding microRNA (miR) dynamics following surgical resection of melanomas is critical to accurately interpret miR changes suggestive of melanoma recurrence. Read More

    Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships.
    Bioinform Biol Insights 2017 23;11:1177932217690136. Epub 2017 Feb 23.
    Department of Agriculture, University of Naples "Federico II," Portici, Italy.
    The detection of orthologs is a key approach in genomics, useful to understand gene evolution and phylogenetic relationships and essential for gene function prediction. However, a reliable annotation of the encoded protein regions is still a limiting aspect in genomics, mainly due to the lack of confirmatory experimental evidence at proteome level. Nevertheless, the current ortholog collections are generally based on protein sequence comparisons, in addition to the availability of large transcriptome sequence collections. Read More

    Current Developments in Machine Learning Techniques in Biological Data Mining.
    Bioinform Biol Insights 2017 22;11:1177932216687545. Epub 2017 Mar 22.
    Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
    This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Read More

    Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, Camelus dromedarius.
    Bioinform Biol Insights 2016 21;10:291-300. Epub 2016 Dec 21.
    National Center for Genomic Technology, King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia.
    Krüppel-like factor 4 (KLF4) is a pluripotency transcription factor that helps in generating induced pluripotent stem cells (iPSCs). We sequenced for the first time the full coding sequence of Camelus dromedarius KLF4 (cKLF4), which is also known as the Arabian camel. Bioinformatics analysis revealed the molecular weight and the isoelectric point of cKLF4 protein to be 53. Read More

    Integrating Epigenomics into the Understanding of Biomedical Insight.
    Bioinform Biol Insights 2016 4;10:267-289. Epub 2016 Dec 4.
    Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
    Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. Read More

    Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.
    Bioinform Biol Insights 2016 30;10:255-265. Epub 2016 Nov 30.
    Department of Computer Science and Engineering, Visvesvaraya National Institute of Technology, Nagpur, India.
    Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. Read More

    Clustering Algorithms: Their Application to Gene Expression Data.
    Bioinform Biol Insights 2016 30;10:237-253. Epub 2016 Nov 30.
    Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria.
    Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Read More

    An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.
    Bioinform Biol Insights 2015 25;9(Suppl 4):59-69. Epub 2016 Oct 25.
    Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.
    A Bayesian method for sampling from the distribution of matches to a precompiled transcription factor binding site (TFBS) sequence pattern (conditioned on an observed nucleotide sequence and the sequence pattern) is described. The method takes a position frequency matrix as input for a set of representative binding sites for a transcription factor and two sets of noncoding, 5' regulatory sequences for gene sets that are to be compared. An empirical prior on the frequency A (per base pair of gene-vicinal, noncoding DNA) of TFBSs is developed using data from the ENCODE project and incorporated into the method. Read More

    Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins.
    Bioinform Biol Insights 2016 30;10:225-236. Epub 2016 Oct 30.
    Instituto de Investigaciones Biológicas y Tecnológicas (IIByT) CONICET-Universidad Nacional de Córdoba, and Instituto de Ciencia y Tecnología de los Alimentos (ICTA), Cátedra de Química Biológica, Departamento de Química Industrial y Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales, Córdoba, Argentina.
    It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca(2+) uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Read More

    Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks.
    Bioinform Biol Insights 2016 25;10:209-224. Epub 2016 Oct 25.
    Researcher, R&D Epigenetics Department of Diagenode SA, Liège, Belgium.
    As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. Read More

    Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum.
    Bioinform Biol Insights 2016 26;10:185-207. Epub 2016 Sep 26.
    Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Cluster of Excellence Macromolecular Complexes, Institute for Molecular Cell Biology of Plants, Frankfurt am Main, Germany.
    Phytohormones control the development and growth of plants, as well as their response to biotic and abiotic stress. The seven most well-studied phytohormone classes defined today are as follows: auxins, ethylene, cytokinin, abscisic acid, jasmonic acid, gibberellins, and brassinosteroids. The basic principle of hormone regulation is conserved in all plants, but recent results suggest adaptations of synthesis, transport, or signaling pathways to the architecture and growth environment of different plant species. Read More

    Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha.
    Bioinform Biol Insights 2016 22;10:167-84. Epub 2016 Sep 22.
    Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India.
    Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. Read More

    Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach.
    Bioinform Biol Insights 2016 29;10:155-66. Epub 2016 Aug 29.
    Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India.
    The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. Read More

    In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.
    Bioinform Biol Insights 2016 14;10:143-54. Epub 2016 Aug 14.
    Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. Read More

    OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.
    Bioinform Biol Insights 2016 2;10:133-41. Epub 2016 Aug 2.
    Department of Genetics and Biochemistry, Clemson University, SC, USA.
    High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U. Read More

    Computational Identification of Novel Genes: Current and Future Perspectives.
    Bioinform Biol Insights 2016 1;10:121-31. Epub 2016 Aug 1.
    Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Huefferstrasse 1, Muenster, Germany.
    While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Read More

    Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2).
    Bioinform Biol Insights 2016 26;10:111-20. Epub 2016 Jul 26.
    National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology, Riyadh, KSA.; SAAD Research and Development Center, Clinical Research Laboratory and Radiation Oncology, SAAD Specialist Hospital, Al Khobar, KSA.
    Although the sequencing information of Sox2 cDNA for many mammalian is available, the Sox2 cDNA of Camelus dromedaries has not yet been characterized. The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). Read More

    PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
    Bioinform Biol Insights 2016 19;10:105-9. Epub 2016 Jul 19.
    National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
    Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. Read More

    Molecular Shape Analysis-Guided Virtual Screening Platform for Adenosine Kinase Inhibitors.
    Bioinform Biol Insights 2016 18;10:97-103. Epub 2016 Jul 18.
    Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
    We propose a new application of molecular shape descriptors in hierarchical selection during virtual screening (VS). Here, a structure-based pharmacophore and docking-guided VS protocol have been evolved to identify inhibitors against adenosine kinase (AK). The knowledge gained on the shape requirements has been extrapolated in classifying active and inactive molecules against this target. Read More

    S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition.
    Bioinform Biol Insights 2016 27;10:81-95. Epub 2016 Jun 27.
    Computation Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, CA, USA.
    Modeling the molecular mechanisms that govern genetic variation can be useful in understanding the dynamics that drive genetic state transition in quasispecies viruses. For example, there is considerable interest in understanding how the relatively benign vaccine strains of poliovirus eventually revert to forms that confer neurovirulence and cause disease (ie, vaccine-derived poliovirus). This report describes a stochastic simulation model, S2M, which can be used to generate hypothetical outcomes based on known mechanisms of genetic diversity. Read More

    PDBparam: Online Resource for Computing Structural Parameters of Proteins.
    Bioinform Biol Insights 2016 14;10:73-80. Epub 2016 Jun 14.
    Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
    Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. Read More

    Genome Data Exploration Using Correspondence Analysis.
    Bioinform Biol Insights 2016 7;10:59-72. Epub 2016 Jun 7.
    Institut Pasteur, Unit of Structural Microbiology, CNRS URA 3528 and University Paris Diderot, Sorbonne Paris Cité, Paris, France.
    Recent developments of sequencing technologies that allow the production of massive amounts of genomic and genotyping data have highlighted the need for synthetic data representation and pattern recognition methods that can mine and help discovering biologically meaningful knowledge included in such large data sets. Correspondence analysis (CA) is an exploratory descriptive method designed to analyze two-way data tables, including some measure of association between rows and columns. It constructs linear combinations of variables, known as factors. Read More

    Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets.
    Bioinform Biol Insights 2016 12;10:49-57. Epub 2016 May 12.
    Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.
    Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. Read More

    Practical Approaches for Mining Frequent Patterns in Molecular Datasets.
    Bioinform Biol Insights 2016 2;10:37-47. Epub 2016 May 2.
    Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.; Biomedical Informatics Research Center Antwerpen (Biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium.
    Pattern detection is an inherent task in the analysis and interpretation of complex and continuously accumulating biological data. Numerous itemset mining algorithms have been developed in the last decade to efficiently detect specific pattern classes in data. Although many of these have proven their value for addressing bioinformatics problems, several factors still slow down promising algorithms from gaining popularity in the life science community. Read More

    Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions.
    Bioinform Biol Insights 2016 28;10:27-35. Epub 2016 Apr 28.
    Mathematics Computation Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia.
    From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Read More

    Use of Metatranscriptomics in Microbiome Research.
    Bioinform Biol Insights 2016 20;10:19-25. Epub 2016 Apr 20.
    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
    The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure. Read More

    Modeling Intercellular Communication as a Survival Strategy of Cancer Cells: An In Silico Approach on a Flexible Bioinformatics Framework.
    Bioinform Biol Insights 2016 13;10:5-18. Epub 2016 Mar 13.
    Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, México.
    Intercellular communication is very important for cell development and allows a group of cells to survive as a population. Cancer cells have a similar behavior, presenting the same mechanisms and characteristics of tissue formation. In this article, we model and simulate the formation of different communication channels that allow an interaction between two cells. Read More

    Transcriptome Analysis in Domesticated Species: Challenges and Strategies.
    Bioinform Biol Insights 2015 16;9(Suppl 4):21-31. Epub 2016 Feb 16.
    Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA.
    Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. Read More

    Visualization of Genome Diversity in German Shepherd Dogs.
    Bioinform Biol Insights 2015 10;9(Suppl 2):37-42. Epub 2016 Feb 10.
    Faculty of Veterinary Science, The University of Sydney, NSW, Australia.
    A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. Read More

    Nematode Sodium Calcium Exchangers: A Surprising Lack of Transport.
    Bioinform Biol Insights 2016 1;10:1-4. Epub 2016 Feb 1.
    Department of Biological Sciences, The George Washington University, Washington, DC, USA.; Institute for Neuroscience, The George Washington University, Washington, DC, USA.
    Na(+)/Ca(2+) exchangers are low-affinity, high-capacity transporters that rapidly transport calcium against a gradient of Na(+) ions. Na(+)/Ca(2+) exchangers are divided into three groups based upon substrate specificity: Na(+)/Ca(2+) exchangers (NCX), Na(+)/Ca(2+)/K(+) exchangers (NCKX), and Ca(2+)/cation exchangers (NCLX). In mammals, there are three NCX genes, five NCKX genes, and a single NCLX gene. Read More

    Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome.
    Bioinform Biol Insights 2015 24;9(Suppl 2):25-36. Epub 2016 Jan 24.
    Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
    This study represents the first swine transcriptome hive plots created from gene set enrichment analysis (GSEA) data and provides a novel insight into the global transcriptome changes occurring in tracheobronchial lymph nodes (TBLN) and spanning the swine genome. RNA isolated from draining TBLN from 5-week-old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected, was interrogated using Illumina Digital Gene Expression Tag Profiling. More than 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6, and 14 days post-inoculation (dpi). Read More

    Evolutionary Character of Alternative Splicing in Plants.
    Bioinform Biol Insights 2015 20;9(Suppl 1):47-52. Epub 2016 Jan 20.
    Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.
    Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. Read More

    Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum.
    Bioinform Biol Insights 2015 20;9:195-206. Epub 2015 Dec 20.
    Department of Physics, Indian Institute of Science, Bangalore, India.
    Plasmodium falciparum, a causative agent of malaria, is a well-characterized obligate intracellular parasite known for its ability to remodel host cells, particularly erythrocytes, to successfully persist in the host environment. However, the current levels of understanding from the laboratory experiments on the host-parasite interactions and the strategies pursued by the parasite to remodel host erythrocytes are modest. Several computational means developed in the recent past to predict host-parasite/pathogen interactions have generated testable hypotheses on feasible protein-protein interactions. Read More

    Sequence Analysis and Evolutionary Studies of Reelin Proteins.
    Bioinform Biol Insights 2015 20;9:187-93. Epub 2015 Dec 20.
    Tata Institute of Fundamental Research, Mumbai, India. ; National Center for Biological Sciences (NCBS), Bengaluru, India.
    The reelin gene is conserved across many vertebrate species, including humans. The protein product of this gene plays several important roles in early brain development and regulation of neural network plasticity of a matured brain structure. With an extended structure of 3461 amino acid sequences, consisting of eight reelin repeats, the human reelin sequence stands out as an exceptional model for evolutionary studies. Read More

    A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor.
    Bioinform Biol Insights 2015 2;9:165-74. Epub 2015 Dec 2.
    Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, One Lomb Memorial Drive, Rochester, NY, USA.
    RNA sequencing (RNA-seq) has revolutionized transcriptome analysis through profiling the expression of thousands of genes at the same time. Systematic analysis of orthologous transcripts across species is critical for understanding the evolution of gene expression and uncovering important information in animal models of human diseases. Several computational methods have been published for analyzing gene expression between species, but they often lack crucial details and therefore cannot serve as a practical guide. Read More

    DDA: A Novel Network-Based Scoring Method to Identify Disease-Disease Associations.
    Bioinform Biol Insights 2015 8;9:175-86. Epub 2015 Dec 8.
    Integrative Bioinformatics and System Biology Group, Advanced Virtual and Intelligent Computing (AVIC) Research Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
    Categorizing human diseases provides higher efficiency and accuracy for disease diagnosis, prognosis, and treatment. Disease-disease association (DDA) is a precious information that indicates the large-scale structure of complex relationships of diseases. However, the number of known and reliable associations is very small. Read More

    Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells.
    Bioinform Biol Insights 2015 25;9:153-64. Epub 2015 Nov 25.
    Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
    The mammalian brain is characterized by distinct classes of cells that differ in morphology, structure, signaling, and function. Dysregulation of gene expression in these cell populations leads to various neurological disorders. Neural cells often need to be acutely purified from animal brains for research, which requires complicated procedure and specific expertise. Read More

    Advanced Applications of RNA Sequencing and Challenges.
    Bioinform Biol Insights 2015 15;9(Suppl 1):29-46. Epub 2015 Nov 15.
    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
    Next-generation sequencing technologies have revolutionarily advanced sequence-based research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq is now being used widely for uncovering multiple facets of transcriptome to facilitate the biological applications. However, the large-scale data analyses associated with RNA-seq harbors challenges. Read More

    Development and Application of a Genetic Algorithm for Variable Optimization and Predictive Modeling of Five-Year Mortality Using Questionnaire Data.
    Bioinform Biol Insights 2015 8;9(Suppl 3):31-41. Epub 2015 Nov 8.
    Department of Chemistry, Oklahoma Baptist University, Shawnee, OK, USA.
    The problem of selecting important variables for predictive modeling of a specific outcome of interest using questionnaire data has rarely been addressed in clinical settings. In this study, we implemented a genetic algorithm (GA) technique to select optimal variables from questionnaire data for predicting a five-year mortality. We examined 123 questions (variables) answered by 5,444 individuals in the National Health and Nutrition Examination Survey. Read More

    The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology.
    Bioinform Biol Insights 2015 23;9(Suppl 1):9-19. Epub 2015 Sep 23.
    Department of Electrical and Computer Engineering, Clemson University, Clemson, SC, USA.
    In the last decade, high-throughput DNA sequencing has become a disruptive technology and pushed the life sciences into a distributed ecosystem of sequence data producers and consumers. Given the power of genomics and declining sequencing costs, biology is an emerging "Big Data" discipline that will soon enter the exabyte data range when all subdisciplines are combined. These datasets must be transferred across commercial and research networks in creative ways since sending data without thought can have serious consequences on data processing time frames. Read More

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